Scientists Unveil New System for Naming Majority of the World’s Microorganisms

Sep 20, 2022 | Announcements, News releases

Scientists Unveil New System for Naming Majority of the World’s Microorganisms

September 20, 2022
LAS VEGAS, Nev.

Microorganisms
SeqCode
Prokaryotes

Above: Fluorescent-stained bacteria (pink) and archaea (green) from near-boiling water from Great Boiling Spring in Gerlach, Nevada. Photo credit: Jeremy Dodsworth.

The SeqCode is a universal system, created through collaboration of hundreds of scientists, to formally register and name single-celled microorganisms known as prokaryotes.

Reposted from https://www.unlv.edu/news/release/scientists-unveil-new-system-naming-majority-worlds-microorganisms.

What’s in a name? For microorganisms, apparently a lot.

Prokaryotes are single-celled microorganisms – bacteria are an example – that are abundant the world over. They exist in the oceans, in soils, in extreme environments like hot springs, and even alongside and inside other organisms including humans.

In short, they’re everywhere, and scientists worldwide are working to both categorize and communicate about them. But here’s the rub: Most don’t have a name.

Less than 0.2% of known prokaryotes have been formally named because current regulations – described in the International Code of Nomenclature of Prokaryotes (ICNP) – require new species to be grown in a lab and freely distributed as pure and viable cultures in collections. Essentially, to name it you have to have multiple physical specimens to prove it.

In an article published Sept. 19 in the journal Nature Microbiology, a team of scientists present a new system, the SeqCode, and a corresponding registration portal that could help microbiologists effectively categorize and communicate about the massive number of identified yet uncultivated prokaryotes.

“Our goal is to unite field and laboratory studies in microbiology and respond to significant recent advancements in environmental genomics by providing a path to formally name the majority of identified yet unnamed prokaryotes,” said UNLV microbiologist Brian Hedlund, lead author on the paper and key collaborator on the development of the SeqCode. “The SeqCode should serve the community by promoting high genome quality standards, good naming practice, and a well-ordered database.”

Creating the SeqCode

Nearly 850 scientists representing multiple disciplines from more than 40 countries participated in a series of NSF-funded online workshops in 2021 to develop the new SeqCode, which uses genome sequence data for both cultivated and uncultivated prokaryotes as the basis for naming prokaryotes.

Since the 2000s, scientists who study prokaryotes in environments all over the world have used environmental genomics techniques to sample and study them, and hundreds of thousands of genome sequences are available in public databases. The community participating in the workshops, which were organized by Hedlund and colleague Anna-Louise Reysenbach from Portland State University, overwhelmingly supported the development of an alternative to the ICNP that would accept DNA sequence data and ultimately improve resources for researchers.

“The key pieces are in place for an orderly expansion of prokaryotic systematics to the entire prokaryotic tree of life,” said William B. Whitman, SeqCode corresponding author and University of Georgia microbiologist. “This expansion will serve the research and the broader community by providing a common language for all prokaryotes that is systematically organized and supported by data-rich genomic datasets and associated metadata.”

To qualify for inclusion in the SeqCode, genomeses must meet rigorous scientific standards to ensure quality, stability, and open data sharing. And, though it’s not yet universally accepted, the SeqCode fundamentally aligns with established international principles for naming other organisms, including plants and animals.

“Any organism with a high-quality genome sequence – from a pure culture or not – can be named under the SeqCode,” said Hedlund. “We will also automatically accept all names formed under the ICNP. I expect through time that the SeqCode will be used much more frequently than the ICNP.”

Creating Clarity Amongst Chaos

One of the primary goals for the new system, authors argue, is to reverse a trend in the field where “unregulated” names are used in literature out of necessity. This can lead to mistakes that increase the likelihood of subsequent renaming later on, making it difficult for scientists to review and compare data and communicate effectively. Conversely, authors argue that the SeqCode “embraces findability, accessibility, interoperability, and reusability principles.”

Hedlund referenced Chlamydia and related organisms as an example. Since these organisms can’t be grown, stored, or distributed as pure cultures, they’re currently unable to be officially named.

“It could be pretty confusing for clinicians to not have valid names for newly discovered chlamydiae,” says Hedlund. “There’s a risk of those names being poorly cataloged, which could stifle tracking of disease outbreaks and communication among scientists, doctors, and the public.”

Overcoming Controversy

Despite its intended goal to create clarity and synergy with accepted standards for naming, the move is not without controversy.

The SeqCode follows a previous attempt by scientists to modify the ICNP to allow uncultivated prokaryotes to be named based on having a DNA sequence that would serve as the evidence (or ‘type’) for the organism – as opposed to the ICNP rules now which require a culture into two permanent collections.

In 2020, a team led by Desert Research Institute biologist Alison Murray published a paper, also in Nature Microbiology, that was co-authored or endorsed by nearly 120 scientists representing 22 countries calling for action on the proposed modifications of the ICNP to accept DNA sequences as types or to go an alternate route. However, the proposed modifications were rejected by the International Committee on Systematics of Prokaryotes, the group responsible for governing the naming of prokaryotes.

“It is clear that the global community of scientists is ready for a paradigm change in how we name prokaryotes – to be inclusive of the breadth of prokaryotic life,” said Murray. “Modern genome technologies can resolve genomes of uncultivated organisms at the high degree of precision needed to ensure integrity and provide stability to the field of microbiology. Naming these taxa is the way to communicate their existence, their evolutionary history and predict their physiological capabilities.”

The 2020 setback led to a redoubling of efforts among the growing cadre of scientists and, ultimately, the “alternative route” which led to the formation of the SeqCode.

“Many people came to the table to share their perspectives, their energy, and their skills to make it happen,” said Hedlund. “The response to our workshops from scientists all over the world was incredible and helped validate why the time has come to formally make a change in how prokaryotes are named.”

Tension still exists among some scientists, who argue that less can be known about uncultivated prokaryotes than those that can be grown and manipulated in a lab as pure cultures. Additionally, nuances in processing and interpreting DNA sequence data could potentially lead to erroneous conclusions, a point that Hedlund claims is also true of studies of pure cultures.

The authors say this new system is not intended to discourage traditional cultivation of prokaryotes, but instead is designed by the scientific community to improve communication across the microbial sciences.

“We view this ‘SeqCode v.1.0’ as a necessary first step toward a unified system of nomenclature to communicate the full diversity of prokaryotes and we will cooperate with the community toward the realization of this vision,” authors write.

More information:

The paper, “SeqCode: a nomenclatural code for prokaryotes described from sequence data” was published Sept. 19 in the journal Nature Microbiology. Learn more about the SeqCode at https://seqco.de/.

###

About DRI

The Desert Research Institute (DRI) is a recognized world leader in basic and applied environmental research. Committed to scientific excellence and integrity, DRI faculty, students who work alongside them, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge on topics ranging from humans’ impact on the environment to the environment’s impact on humans. DRI’s impactful science and inspiring solutions support Nevada’s diverse economy, provide science-based educational opportunities, and inform policymakers, business leaders, and community members. With campuses in Las Vegas and Reno, DRI serves as the non-profit research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.

About UNLV

UNLV is a doctoral-degree-granting institution of more than 30,000 students and nearly 4,000 faculty and staff that has earned the nation’s highest recognition for both research and community engagement from the Carnegie Foundation for the Advancement of Teaching. UNLV offers a broad range of respected academic programs and is committed to recruiting and retaining top students and faculty, educating the region’s diverse population and workforce, driving economic activity, and creating an academic health center for Southern Nevada. Learn more at unlv.edu.

Heading to the mountains? The Living Snow Project needs your help

Jul 8, 2022 | Blog, Featured researchers

Heading to the Mountains?

The Living Snow Project needs your help

JULY 8, 2022
RENO, NEV.

By Kelsey Fitzgerald

Living Snow Project
Snow Algae
Citizen Science

Featured research by DRI’s Alison Murray, Meghan Collins, Jaiden Christopher, Eric Lundin, and Sonia Nieminen.

On a cool and breezy morning in late spring, DRI Research Professor Alison Murray, Ph.D. and student intern Sonia Nieminen hiked up a ski slope at Mount Rose Ski Area, outside of Reno. The ground, wet from snowmelt, squished and squelched beneath their feet as they crossed a hillside of soggy grass to reach a remnant patch of late-season snow.

They were out to find snow algae – a type of freshwater algae that thrives in late-season snowpack. Although snow algae is best known for being pink, it actually comes in colors ranging from yellow to orange, light-green, brown, light pink, or a bright watermelon pink.

“There’s a whole microbial community that lives in the snow, and snow algae is the food source that gets it all started,” Murray explained. “They are a primary producer, so they bring organic carbon into the snow that feeds a diverse community of bacteria, fungi, protozoans and other multicellular animals. For example, little rotifers, tartigrades, mites, and spiders also call the snow ecosystem home.”

Alison Murray, Sonia Nieminen, and KOLO reporter John Macaluso look for snow algae among snow patches at Mount Rose, May 31, 2022.

Credit: DRI.

Murray, Nieminen, Meghan Collins, Jaiden Christopher, and Eric Lundin at DRI are studying snow algae as part of the Living Snow Project (https://wp.wwu.edu/livingsnowproject/) – a collaboration between DRI and Robin Kodner and her team at Western Washington University. The project aims to learn more about the ecology, diversity, and prevalence of snow algae in the Cascade and Sierra Nevada mountains, with help from citizen scientists.

“The literature is pretty spotty on the biology of snow and snow algae,” Murray said. “A lot is known about just a few species of snow algae, but we want to see what else is out there, and learn more about the role that algae play in the snowpack in a changing climate.”

female scientist digs through patch of light pink snow

Alison Murray digs into a patch of light pink snow at Mount Rose Ski Area to collect a snow algae sample.

Credit: DRI.

To collect a sample of snow algae, Murray and Nieminen first looked for patches of discolored snow. They dug down a few inches with a shovel, and then opened a sample collection kit – a pair of rubber gloves and a small plastic tube filled with a small amount of preservative. They used the lid of the tube to scoop some snow into the tube, then gave it a shake and sealed it. Finally, they recorded their location and sample number using the project’s smartphone app.

Living Snow Project sample collection kit instructions

Top Left: Participants in the Living Snow Project receive sample collection kits with specific instructions on how to collect a snow algae sample.

Top Right: Snow algae samples are collected using a plastic tube filled with a small amount of preservative.

Bottom: Sonia Nieminen collects a snow algae sample at Mount Rose Ski Area.

Credit: DRI.

Just off the boardwalk at Tahoe Meadows, the team came across another patch of lightly pink pigmented snow and stopped to collect some samples. Snow algae spend the winter in the soil, Murray explained, and remain there until the wetness and light conditions of melting snowpack trigger the algae’s flagellated growth phase. The algae move to the top of the snowpack, where they develop sunscreen-like pigments that turn them shades of orange, pink, or deep red.

Scientist collects snow algae with rubber gloves

Sample tubes with snow algae inside on top of snow

Top Left: DRI scientist Alison Murray collects a snow algae sample at Tahoe Meadows.

Top Right: Sonia Nieminen collects a snow algae sample at Tahoe Meadows. Rubber gloves help to prevent the contamination of samples with any microbiota on the researcher’s hands.

Bottom: Samples tubes containing snow algae collected at Tahoe Meadows in Nevada during late spring 2022.

Credit: DRI.

In the sample tubes, the snow samples appeared muted shades of brown, yellow, and light pink. But back in the laboratory at DRI, Eric Lundin placed the samples under a light microscope, and the red pigments became easier to see.

“The algae appear red due to astaxanthin, a pigment that protects snow algae from UV radiation,” Lundin explained.

Next, he examined the samples using fluorescence microscopy and DAPI staining. DAPI is a fluorescent dye that is attracted to DNA. Using fluorescence microscopy, the snow algae appear as red circular cells due to the autofluorescence of chlorophyll.

Finally, he looked at the samples using confocal microscopy, which uses specific wavelengths of light to induce fluorescence and shows the 3-D structure of the cells as a 2-D image. In these images, blue indicates the presence of DNA. Chlorophyll appears red, clearly showing the presence of snow algae. The snow algae cells are often coated with a layer of bacterial cells, and some debris too.

Snow algae cells viewed with a microscopy

Top Left: Snow algae cells (red) from the Mount Rose sites were identified in the laboratory using a light microscope. Pollen grains are large and appear to have two “ears” on either side of the main pollen particle, that helps the pollen grains get transported by the wind, they are often referred to as Mickey-Mouse shaped.

Top Right: Using fluorescence microscopy and DAPI staining to examine a sample, snow algae appear as red circular cells. Pollen grains, if the nucleus is still intact, emit blue light due to the presence of DNA. Other material seen in the image is a combination of bacteria, plants, dirt, and extracellular material.

Bottom: Snow algae, some of which are surrounded by bacterial cells (blue) as viewed with confocal microscopy. Blue indicates the presence of DNA, and red indicates presence of chlorophyll.

Credit: DRI

Want to participate in the Living Snow Project?

For the second year in a row, the group has put out a call to action to the outdoor recreation community for help tracking snow algae blooms, recording observations, and collecting samples of snow algae from backcountry areas during the late spring into the summer. By enlisting the help of volunteers, the research team is able to cover much more ground than they could alone.

“We appreciate the help of anyone who is out in the mountains in the early summer – hikers, summer skiers, or anyone else – who can help us collect samples or just use their phones to log locations where snow algae is found and how prevalent it is,” Murray said.

Are you heading to the mountains and interested in participating in the Living Snow Project? Instructions for how to participate are available on the Living Snow website: https://wp.wwu.edu/livingsnowproject/

Media coverage:

https://www.kolotv.com/2022/06/21/dri-working-with-community-collect-snow-algae-samples/

###

About DRI

The Desert Research Institute (DRI) is a recognized world leader in basic and applied environmental research. Committed to scientific excellence and integrity, DRI faculty, students who work alongside them, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge on topics ranging from humans’ impact on the environment to the environment’s impact on humans. DRI’s impactful science and inspiring solutions support Nevada’s diverse economy, provide science-based educational opportunities, and inform policymakers, business leaders, and community members. With campuses in Las Vegas and Reno, DRI serves as the non-profit research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.

Within an Antarctic Sea Squirt, Scientists Discover a Bacterial Species With Promising Anti-Melanoma Properties

Nov 22, 2021 | News releases, Research findings

Within an Antarctic Sea Squirt, Scientists Discover a Bacterial Species With Promising Anti-Melanoma Properties

December 1, 2021
RENO, NEV.

By Kelsey Fitzgerald

Antarctic Sea Squirt
Melanoma
Health

Above: Late spring at Arthur Harbor. The waters surrounding Anvers Island, Antarctica, are home to a species of sea squirt called Synoicum adareanum. New research has traced the production of palmerolide A, a key compound with anti-melanoma properties, to a member of this sea squirt’s microbiome.

Credit: Alison E. Murray, DRI

New study brings important advances for Antarctic science and natural products chemistry

There are few places farther from your medicine cabinet than the tissues of an ascidian, or “sea squirt,” on the icy Antarctic sea floor – but this is precisely where scientists are looking to find a new treatment for melanoma, one of the most dangerous types of skin cancer.

In a new paper that was published today in mSphere, a research team from DRI, Los Alamos National Laboratory (LANL), and the University of South Florida (USF) made strides toward their goal, successfully tracing a naturally-produced melanoma-fighting compound called “palmerolide A” to its source: a microbe that resides within Synoicum adareanum, a species of ascidian common to the waters of Antarctica’s Anvers Island archipelago.

“We have long suspected that palmerolide A was produced by one of the many types of bacteria that live within this ascidian host species, S. adareanum,” explained lead author Alison Murray, Ph.D., research professor of biology at DRI. “Now, we have actually been able to identify the specific microbe that produces this compound, which is a huge step forward toward developing a naturally-derived treatment for melanoma.”

Synoicum adareanum in 80 feet of water at Bonaparte Point, Antarctica. New research has traced the production of palmerolide A, a key compound with anti-melanoma properties, to a suite of genes coded in the genome by a member of this sea squirt’s microbiome.

Credit: Bill J. Baker, University of South Florida.

Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

The full study, Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with anti-melanoma palmerolide biosynthetic potential, is available from mSphere.

The bacterium that the team identified is a member of a new and previously unstudied genus, Candidatus Synoicihabitans palmerolidicus. This advance in knowledge builds on what Murray and her colleagues have learned across more than a decade of research on palmerolide A and its association with the microbiome (collective suite of microbes and their genomes) of the host ascidian, S. adareanum.

In 2008, Murray worked with Bill Baker, Ph.D., professor of chemistry at USF and Christian Riesenfeld, Ph.D., postdoctoral researcher at DRI to publish a study on the microbial diversity of a single S. adareanum organism. In 2020, the team expanded to include additional researchers from LANL, USF, and the Université de Nantes, and published new work identifying the “core microbiome” of S. adareanum – a common suite of 21 bacterial species that were present across 63 different samples of S. adareanum collected from around the Anvers Island archipelago.

In the team’s latest research, they looked more closely at the core microbiome members identified in their 2020 paper to determine which of the 21 types of bacteria were responsible for the production of palmerolide A. They conducted several rounds of environmental genome sequencing, followed by automated and manual assembly, gene mining, and phylogenomic analyses, which resulted in the identification of the biosynthetic gene cluster and palmerolide A-producing organism.

“This is the first time that we’ve matched an Antarctic natural product to the genetic machinery that is responsible for its biosynthesis,” Murray said. “As an anti-cancer therapeutic, we can’t just go to Antarctica and harvest these sea squirts en masse, but now that we understand the underlying genetic machinery, it opens the door for us to find a biotechnological solution to produce this compound.”

“Knowing the producer of palmerolide A enables cultivation, which will finally provide sufficient quantity of the compound for needed studies of its pharmacological properties,” added Baker.

A diver collects samples of Synoicum adareanum in support of a microbiome and biosynthetic gene cluster study. Palmer Station Antarctica, March 2011.

Credit: Bill Dent, University of South Florida.

Many additional questions remain, such as how S. adareanum and its palmerolide-producing symbiont are distributed across the landscape in Antarctic Oceans, or what role palmerolide A plays in the ecology of this species of ascidian. Likewise, a detailed investigation into how the genes code for the enzymes that make palmerolide A is the subject of a new report soon to be published.

To survive in the harsh and unusual environment of the Antarctic sea floor, ascidians and other invertebrates such as sponges and corals have developed symbiotic relationships with diverse microbes that play a role in the production of features such as photoprotective pigments, bioluminescence, and chemical defense agents. The compounds produced by these microbes may have medicinal and biotechnological applications useful to humans in science, health and industry. Palmerolide A is one of many examples yet to be discovered.

“Throughout the course of disentangling the many genomic fragments of the various species in the microbiome, we discovered that this novel microbe’s genome appears to harbor multiple copies of the genes responsible for palmerolide production,” said Patrick Chain, Ph.D., senior scientist and Laboratory Fellow with LANL. “However the role of each copy, and regulation, for example, are unknown. This suggests palmerolide is likely quite important to the bacterium or the host, though we have yet to understand it’s biological or ecological role within this Antarctic setting.”

“This is a beautiful example of how nature is the best chemist out there,” Murray added. “The fact that microbes can make these bioactive and sometimes toxic compounds that can help the hosts to facilitate their survival is exemplary of the evolutionary intricacies found between hosts and their microbial partners and the chemical handshakes that are going on under our feet on all corners of the planet.”

Andrew Schilling (University of South Florida) dives in 100 feet of water at Cormorant Wall, Antarctica. Samples for microbiome characterization were collected by SCUBA divers working in the chilly subzero seas off Anvers Island, in the Antarctic Peninsula.

Credit: Bill J. Baker, University of South Florida.

More information:

The full study, Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential, is available from mSphere.

Study authors included Alison Murray (DRI), Chein-Chi Lo (LANL), Hajnalka E. Daligault (LANL), Nicole E. Avalon (USF), Robert W. Read (DRI), Karen W. Davenport (LANL), Mary L. Higham (DRI), Yuliya Kunde (LANL), Armand E.K. Dichosa (LANL), Bill J. Baker (USF), and Patrick S.G. Chain (LANL).

This study was made possible with funding from the National Institutes of Health (CA205932), the National Science Foundation (OPP-0442857, ANT-0838776, and PLR-1341339), and DRI (Institute Project Assignment).

###

About DRI

The Desert Research Institute (DRI) is a recognized world leader in basic and applied environmental research. Committed to scientific excellence and integrity, DRI faculty, students who work alongside them, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge on topics ranging from humans’ impact on the environment to the environment’s impact on humans. DRI’s impactful science and inspiring solutions support Nevada’s diverse economy, provide science-based educational opportunities, and inform policymakers, business leaders, and community members. With campuses in Las Vegas and Reno, DRI serves as the non-profit research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.

About The University of South Florida

The University of South Florida is a high-impact global research university dedicated to student success. Over the past 10 years, no other public university in the country has risen faster in U.S. News and World Report’s national university rankings than USF. Serving more than 50,000 students on campuses in Tampa, St. Petersburg and Sarasota-Manatee, USF is designated as a Preeminent State Research University by the Florida Board of Governors, placing it in the most elite category among the state’s 12 public universities. USF has earned widespread national recognition for its success graduating under-represented minority and limited-income students at rates equal to or higher than white and higher income students. USF is a member of the American Athletic Conference. Learn more at www.usf.edu.

About Los Alamos National Laboratory

Los Alamos National Laboratory, a multidisciplinary research institution engaged in strategic science on behalf of national security, is managed by Triad, a public service oriented, national security science organization equally owned by its three founding members: Battelle Memorial Institute (Battelle), the Texas A&M University System (TAMUS), and the Regents of the University of California (UC) for the Department of Energy’s National Nuclear Security Administration. Los Alamos enhances national security by ensuring the safety and reliability of the U.S. nuclear stockpile, developing technologies to reduce threats from weapons of mass destruction, and solving problems related to energy, environment, infrastructure, health, and global security concerns.

New study reveals key information about the microbiome of an important anticancer compound-producing Antarctic marine invertebrate

Jun 25, 2020 | News releases, Research findings

New study reveals key information about the microbiome of an important anticancer compound-producing Antarctic marine invertebrate

RENO, NEV.
JUNE 25, 2020

Microbiology
Melanoma
Ascidians

Could the cure for melanoma – the most dangerous type of skin cancer – be a compound derived from a marine invertebrate that lives at the bottom of the ocean? A group of scientists led by Alison Murray, Ph.D. of the Desert Research Institute (DRI) in Reno think so, and are looking to the microbiome of an Antarctic ascidian called Synoicum adareanum to better understand the possibilities for development of a melanoma-specific drug.

Ascidians, or “sea squirts”, are primitive, sac-like marine animals that live attached to ocean-bottoms around the world, and feed on plankton by filtering seawater. S. adareanum, which grows in small colonies in the waters surrounding Antarctica, is known to contain a bioactive compound called “Palmerolide A” with promising anti-melanoma properties – and researchers believe that the compound is produced by bacteria that are naturally associated with S. adareanum.

In a new paper published this month in the journal Marine Drugs, Murray and collaborators from the University of South Florida, the Los Alamos National Laboratory, and the Université de Nantes, France, present important new findings measuring palmerolide levels across samples collected from Antarctica’s Anvers Island Archipelago and characterizing the community of bacteria that make up the microbiome of S. adareanum.

“Our longer-term goal is to figure out which of the many bacteria within this species is producing palmerolide, but to do this, there is a lot we need to learn about the microbiome of S. adareanum,” Murray said. “Our new study describes many advances that we have made toward that goal over the last few years.”

Synoicum adareanum: The Antarctic sea squirt, Synoicum adareanum at 80’ (24 meters) lives amongst the red algae, bryozoans and starfish on the seafloor. It is a non-motile benthic species that gets its nutrition from microorganisms and organic carbon in the seawater. Its microbiome hosts a suite of different microorganisms that can provide defenses against predation and infection in some cases. Tissues of this animal were found to contain high levels of a compound that is active against melanoma, which is thought to be produced by a member of the sea squirt’s microbiome.

Credit: Bill Baker, USF

Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica. (click to view article)

In 2008, Murray worked with Bill Baker, Ph.D., of the University of South Florida, and DRI postdoctoral researcher Christian Riesenfeld, Ph.D., to publish a study on the microbial diversity of one individual S. adareanum. Their new study builds upon this research by characterizing the microbial diversity of 63 different individuals that were collected from around Anvers Island.

Their results identify a what the researchers call the “core microbiome” of the species – a common suite of 21 bacterial taxa that were present in more than 80 percent of samples, and six bacterial taxa that were present in all 63 samples.

“It is a key “first” for Antarctic science to have been able to find and identify this core microbiome in a fairly large regional study of these organisms,” Murray said. “This is information that we need to get to the next step of identifying the producer of palmerolide.”

Another “first” for Antarctic science, and for the study of natural products in nature in general, was a comparison of palmerolide levels across all 63 samples that showed the compound was present in every specimen at high (milligram per gram specimen tissue) levels, but the researchers found no trends between sites, samples, or microbiome bacteria. Additional analysis looking at the co-occurrence relationships of the taxa across the large data set showed some of the ways that bacteria are interacting with each other and with the host species in this marine ecosystem.

“The microbiome itself is unique in composition from other ascidians, and seems to be pretty interesting, with a lot of interaction,” Murray said. “Our study has opened the doors to understand the ecology of this system.”

From the assemblage of bacteria that the researchers have identified as making up the core microbiome of S. adareanum, they next hope to use a genomics approach to finally be able to identify which of the bacteria are producing palmerolide – an important and needed advancement toward the development of a melanoma treatment.

“It would be a really big deal to use this compound to develop a drug for fighting melanoma, because there are just so few drugs at the moment that can be used to treat it,” Murray said. “If we can identify the bacteria that produce this chemical, and with its genome understand how to cultivate it in a laboratory setting, this would enable us to provide a sustainable supply of palmerolide that would not rely on harvesting wild populations of this species in Antarctica.”

Anvers Island Antarctica: Samples for microbiome characterization were collected by SCUBA divers working on the sea ice off Anvers Island, in the Antarctic Peninsula. Diving through holes cut in the sea ice requires dry suites, and relatively short dive times. (photographed Prof. Bill Baker in the hole, and his graduate student Chris Petri suited on the sled).

Credit: Maggy Amsler

DNA-stained micrograph: Cultivation efforts led to isolation of a new bacterial species affiliated with the Pseudovibrio genus – a group known to produce bioactive compounds – this is the first cold-adapted member of this genus. This strain has unusual branching morphology (seen in the DNA-stained micrograph), and storage granules that appear yellow.

Credit: Eric Lundin, DRI

“It is a key “first” for Antarctic science to have been able to find and identify this core microbiome in a fairly large regional study of these organisms,” Murray said. “This is information that we need to get to the next step of identifying the producer of palmerolide.”

Additional information

The full text of the study, “Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica,” is available from Marine Drugs: https://www.mdpi.com/1660-3397/18/6/298/htm

This research was supported by the National Institute of Health, National Cancer Institute, and the National Science Foundation.

###

About the Desert Research Institute

The Desert Research Institute (DRI) is a recognized world leader in basic and applied interdisciplinary research. Committed to scientific excellence and integrity, DRI faculty, students, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge, supported Nevada’s diversifying economy, provided science-based educational opportunities, and informed policy makers, business leaders, and community members. With campuses in Reno and Las Vegas, DRI serves as the non-profit research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.

Media Contact

Justin Broglio
Communications Manager, Desert Research Institute
775-762-8320
Justin.Broglio@dri.edu
@DRIScience

International Consortium of Scientists Propose New Naming System for Uncultivated Bacteria and Archaea

Jun 8, 2020 | News releases, Research findings

International Consortium of Scientists Propose New Naming System for Uncultivated Bacteria and Archaea

RENO, NEV.
JUNE 8, 2020

Microbiology
Nomenclature
Taxonomy

The long-standing rules for assigning scientific names to bacteria and archaea are overdue for an update, according to a new consensus statement backed by 119 microbiologists from around the globe.

Bacteria and archaea (single-celled organisms that lack cell nuclei) make up two of the three domains of life on Earth, and are named according to the International Code of Nomenclature of Prokaryotes (ICNP; the Code). At present, the Code only recognizes species that can be grown from cultures in laboratories – a requirement that has long been problematic for microbiologists who study bacteria and archaea in the wild.

Since the 1980s, microbiologists have used genetic sequencing techniques to sample and study DNA of microorganisms directly from the environment, across diverse habitats ranging from Earth’s icy oceans to deep underground mines to the surface of human skin. For a vast majority of these species, no method yet exists for cultivating them in a laboratory, and thus, according to the Code, they cannot be officially named.

“There has been a surge in recent years in genome-based discoveries for archaea and bacteria collected from the environment, but no system in place to formally name them, which is creating a lot of chaos and confusion in the field,” said Alison Murray, Ph.D., Research Professor of Biology at the Desert Research Institute (DRI) in Reno. “Being able to represent the diversity of uncultivated organisms known by their genome sequences in a common language is incredibly important.”

Deep-sea hydrothermal vent chimney from the Mid-Atlantic Ridge. Many new microbial genomes have been described from these environments.

Credit: Anna-Louise Reysenbach and Woods Hole Oceanographic Institution.

Consensus Statement: Roadmap for naming uncultivated Archaea and Bacteria (click to view article)

In an article published this week in the journal Nature Microbiology, Murray and her collaborators present the rationale for updating the existing regulations for naming new species of bacteria and archaea, and propose two possible paths forward.

As a first option, the group proposes formally revising the Code to include uncultivated bacteria and archaea represented by DNA sequence information, in place of the live culture samples that are currently required. As an alternative, they propose creating an entirely separate naming system for uncultivated organisms that could be merged with the Code at some point in the future.

“For researchers in this field, the benefits of moving forward with either of these options will be huge,” said Brian Hedlund, Ph.D., Professor of Life Sciences at the University of Nevada, Las Vegas. “We will be able to create a unified list of all of the uncultivated species that have been discovered over the last few decades and implement universal quality standards for how and when a new species should be named.”

For example, researchers who use DNA sequencing to study the human microbiome – the thousands of species of Bacteria and Archaea that that live inside and on the human body – would have a means of assigning formal names to the species they identify that are not yet represented in culture collections. This would improve the ability for researchers around the world to conduct collaborative studies on topics such as connections between diet and gut bacteria in different human populations, or to build off of previous research.

This micrograph is a representative Antarctic marine sample of bacteria and archaea that has been stained with a fluorescent dye (DAPI) that binds to DNA. A typical sample of Antarctic seawater harbors 200 to over 600 different taxa based on the diversity of 16S rRNA gene sequences. Only a small fraction of this diversity, < 1%, has been cultivated, or matches sequences of cultivated bacteria and archaea in publicly accessible databases. Through developing a nomenclature system that represents the uncultivated majority, a path for communicating diversity will benefit particularly, those microbial scientists working in natural, bio-engineered, and host-associated ecosystems.

Credit: Alison Murray/DRI.

A proposed update to the International Code of Nomenclature of Prokaryotes would allow scientists to assign official names to uncultivated species of Bacteria and Archaea, such as the specimens shown in this enrichment culture of heat-loving Bacteria and Archaea from a hot spring.

Credit: Anna-Louise Reysenbach.

“It sets the framework for a path forward to provide a structured way to communicate the vast untapped biodiversity of the microbial world within the scientific community and across the public domain” said Anna-Louise Reysenbach, Ph.D., Professor of Biology at Portland State University. “That’s why this change is so important.”

The article and proposed plans are the culmination of a series of workshops that were funded by the National Science Foundation. The next step, says Murray, is to figure out an implementation strategy for moving forward with one of the two proposed plans, while engaging the many microbiologists who contributed to this consensus statement and others around the world who want to help see this change enacted. So far, many have been eager to participate.

“This is an exciting field to be in right now because we’re describing diversity of life on Earth and uncovering new phyla just like scientists were back in the 1800s when they were still discovering larger organisms,” Murray said. “Lots of paradigms have been changing in how we understand the way the world works, and how much diversity is out there – and this is another change that needs to be made. We’re going to need to change it or we’re going to live in chaos.”

“Lots of paradigms have been changing in how we understand the way the world works, and how much diversity is out there – and this is another change that needs to be made. We’re going to need to change it or we’re going to live in chaos.”

Additional information

This project was supported by the National Science Foundation. Additional authors included DRI’s Duane Moser, Ph.D.

To view the full text of the aricle “Roadmap for naming uncultivated Archaea and Bacteria” in Nature Microbiology, please visit: https://www.nature.com/articles/s41564-020-0733-x

For more information on lead author Alison Murray, Ph.D. and her research, please visit: https://www.dri.edu/alison-murray-research/

###

About the Desert Research Institute

The Desert Research Institute (DRI) is a recognized world leader in basic and applied interdisciplinary research. Committed to scientific excellence and integrity, DRI faculty, students, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge, supported Nevada’s diversifying economy, provided science-based educational opportunities, and informed policy makers, business leaders, and community members. With campuses in Reno and Las Vegas, DRI serves as the non-profit research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.

Media Contact

Kelsey Fitzgerald
Science Writer, Desert Research Institute
775-741-0496
Kelsey.Fitzgerald@dri.edu
@DRIScience

Alison Murray selected to co-lead NASA’s Network for Ocean Worlds

Jun 24, 2019 | Announcements, News releases

New initiative will guide search for life in ice-covered water worlds beyond Earth

(Reno, Nevada – June 24, 2019) – Desert Research Institute microbial oceanographer and Antarctic researcher Alison Murray, Ph.D., has been selected to co-lead a new National Aeronautics and Space Administration (NASA) initiative to guide the search for life in ocean worlds beyond Earth.

The Network for Ocean Worlds (NOW) is the latest of four research coordination networks (RCNs) to be established by NASA, introduced today at AbSciCon 2019 in Seattle, Washington. NOW will foster research to identify ice-covered ocean worlds beyond Earth, characterize those oceans, investigate their habitability, search for life, and ultimately understand any life that is found.

“Ocean worlds beyond Earth have been a key research focus for NASA’s Planetary Science Division ever since the confirmation of ice-covered liquid water oceans on Jupiter’s moons,” explained Murray, who is best known for her work discovering the existence of microbial life at −13 °C within the ice-sealed Lake Vida in Antarctica in 2013.

Murray’s research has redefined the scientific view of biological diversity in Earth’s most extreme environments and provided critical insights into how microorganisms persist and function in extremely cold and harsh settings, including those that lack oxygen and biological sources of energy.

Murray will co-lead the network with Chris German at the Woods Hole Oceanographic Institution (WHOI) and Alyssa Rhoden at the Southwest Research Institute (SwRI).

“This new research coordination network will broaden our base of oceanographic expertise throughout the field of astrobiology by creating new collaborations and partnerships that will engage other federal agencies, international partners, philanthropic organizations and relevant NGOs,” added Murray. “This is an exciting time to both advance understanding of life in Earth’s polar ecosystems, and apply this understanding to cryospheres in ocean worlds of places like Europa, Enceladus and Titan.”

NOW will provide a forum for exchange of ideas and learning across the interdisciplinary spectrum of backgrounds and perspectives represented within the network of NASA-funded ocean worlds investigators.

“If we hope to find evidence of life beyond Earth, within the next human generation, then our best bet is to look toward the growing list of ice-covered ocean worlds right here in our own solar system,” said German. “And looking further ahead, if we want to understand the range of possible conditions that could support life anywhere beyond Earth, then we will simultaneously need to both continue exploring our own ocean for examples of extremes under which life can exist and continue developing exploration technologies that will be useful on/any/ocean world, including Earth.”

NOW’s first major focus will be to enhance the development of future NASA missions to Ocean Worlds, beginning with the Europa Clipper mission set to launch in June 2023.